Negombata ceramide 1b - Compound Card

Negombata ceramide 1b

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Negombata ceramide 1b

Structure
Zoomed Structure
  • Family: Animalia - Niphatidae
  • Kingdom: Animalia
  • Class: Ceramide
Canonical Smiles CCCCCCCCCCCCCCCCCC(=O)N[C@H]([C@@H]([C@@H](CCCCCCCCCCCCCCCCC(C)C)O)O)CO
InChI InChI=1S/C41H83NO4/c1-4-5-6-7-8-9-10-11-12-17-20-23-26-29-32-35-40(45)42-38(36-43)41(46)39(44)34-31-28-25-22-19-16-14-13-15-18-21-24-27-30-33-37(2)3/h37-39,41,43-44,46H,4-36H2,1-3H3,(H,42,45)/t38-,39+,41-/m0/s1
InChIKey HSVYFTJBYZCXTB-CUVPNIRJSA-N
Formula C41H83NO4
HBA 4
HBD 4
MW 654.12
Rotatable Bonds 37
TPSA 89.79
LogP 11.34
Number Rings 0
Number Aromatic Rings 0
Heavy Atom Count 46
Formal Charge 0
Fraction CSP3 0.98
Exact Mass 653.63
Number of Lipinski Rule Violations 2
# Species Family Kingdom NCBI Taxonomy ID
1 Negombata corticata Podospongiidae Animalia 81543
2 Amphimedon sp. Niphatidae Animalia 178513

Showing of synonyms

  • Ahmed SA, Khalifa SI, et al. (2008). Antiepileptic ceramides from the Red Sea sponge Negombata corticata. Journal of Natural Products,2008,71(4),513-515. [View]
  • Shady N.H, Abdelmohsen U.R, et al. (2021). Cytotoxic potential of the Red Sea sponge Amphimedon sp. supported by in silico modelling and dereplication analysis. Natural product research, 2021, 35(24), 6093-6098. [View] [PubMed]
Pubchem: 24862371
Nmrshiftdb2: 70032075

No compound-protein relationship available.

No scaffolds available.

Antiepileptic

Absorption

Caco-2 (logPapp)
-5.31
Human Oral Bioavailability 20%
Non-Bioavailable
Human Intestinal Absorption
Absorbed
Madin-Darby Canine Kidney
-4.67
Human Oral Bioavailability 50%
Non-Bioavailable
P-Glycoprotein Inhibitor
Non-Inhibitor
P-Glycoprotein Substrate
Substrate
Skin Permeability
13.61

Distribution

Blood-Brain Barrier (CNS)
-
Blood-Brain Barrier
Non-Penetrable
Fraction Unbound (Human)
2.08
Plasma Protein Binding
71.29
Steady State Volume of Distribution
-

Metabolism

Breast Cancer Resistance Protein
Non-Inhibitor
CYP 1A2 Inhibitor
Non-Inhibitor
CYP 1A2 Substrate
Non-Substrate
CYP 2C19 Inhibitor
Non-Inhibitor
CYP 2C19 Substrate
Non-Substrate
CYP 2C9 Inhibitor
Non-Inhibitor
CYP 2C9 Substrate
Non-Substrate
CYP 2D6 Inhibitor
Non-Inhibitor
CYP 2D6 Substrate
Non-Substrate
CYP 3A4 Inhibitor
Non-Inhibitor
CYP 3A4 Substrate
Non-Substrate
OATP1B1
Non-Inhibitor
OATP1B3
Inhibitor

Excretion

Clearance
1.33
Organic Cation Transporter 2
Non-Inhibitor
Half-Life of Drug
-

Toxicity

AMES Mutagenesis
Safe
Avian
Safe
Bee
Safe
Bioconcentration Factor
-1.1
Biodegradation
Safe
Carcinogenesis
Safe
Crustacean
Toxic
Liver Injury I (DILI)
Toxic
Eye Corrosion
Safe
Eye Irritation
Safe
Maximum Tolerated Dose
0.11
Liver Injury II
Safe
hERG Blockers
Toxic
Daphnia Maga
4.35
Micronucleos
Safe
NR-AhR
Safe
NR-AR
Safe
NR-AR-LBD
Safe
NR-Aromatase
Safe
NR-ER
Safe
NR-ER-LBD
Safe
NR-GR
Safe
NR-PPAR-gamma
Safe
NR-TR
Safe
T. Pyriformis
-30926.67
Rat (Acute)
1.97
Rat (Chronic Oral)
3.7
Fathead Minnow
56.0
Respiratory Disease
Safe
Skin Sensitisation
Toxic
SR-ARE
Safe
SR-ATAD5
Safe
SR-HSE
Safe
SR-MMP
Safe
SR-p53
Safe

General Properties

Boiling Point
1403.83
Hydration Free Energy
-2.92
Log(D) at pH=7.4
6.44
Log(P)
15.68
Log S
-7.11
Log(Vapor Pressure)
-24.4
Melting Point
94.39
pKa Acid
9.49
pKa Basic
5.08
Protein Name UniProt ID Entry Name Species #Pharmacophore Points Probability (0.7 ≤ Tversky Score ≤ 1.0)
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8983
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8983
Serpin domain-containing protein H0ZQY2 H0ZQY2_TAEGU Taeniopygia guttata 3 0.8929
Serpin domain-containing protein H0ZQY2 H0ZQY2_TAEGU Taeniopygia guttata 3 0.8929
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8876
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8876
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8762
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8762
Macrophage metalloelastase P39900 MMP12_HUMAN Homo sapiens 3 0.8741
Macrophage metalloelastase P39900 MMP12_HUMAN Homo sapiens 3 0.8741
4-alpha-glucanotransferase O87172 MALQ_THETH Thermus thermophilus 3 0.8734
4-alpha-glucanotransferase O87172 MALQ_THETH Thermus thermophilus 3 0.8734
Iota toxin component Ia Q46220 Q46220_CLOPF Clostridium perfringens 3 0.8666
Iota toxin component Ia Q46220 Q46220_CLOPF Clostridium perfringens 3 0.8666
Aldos-2-ulose dehydratase P84193 AUD_PHACH Phanerodontia chrysosporium 3 0.8607
Aldos-2-ulose dehydratase P84193 AUD_PHACH Phanerodontia chrysosporium 3 0.8607
Beta-glucosidase A Q08638 BGLA_THEMA Thermotoga maritima 4 0.8479
Beta-glucosidase A Q08638 BGLA_THEMA Thermotoga maritima 4 0.8479
Lysosomal acid glucosylceramidase P04062 GLCM_HUMAN Homo sapiens 3 0.8173
Lysosomal acid glucosylceramidase P04062 GLCM_HUMAN Homo sapiens 3 0.8173
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8171
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 3 0.8171
Beta-glucosidase Q8T0W7 Q8T0W7_9NEOP Neotermes koshunensis 3 0.7887
Beta-glucosidase Q8T0W7 Q8T0W7_9NEOP Neotermes koshunensis 3 0.7887
Beta-glucosidase A Q08638 BGLA_THEMA Thermotoga maritima 3 0.7840
Beta-glucosidase A Q08638 BGLA_THEMA Thermotoga maritima 3 0.7840
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 4 0.7806
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 4 0.7806
Beta-galactosidase P00722 BGAL_ECOLI Escherichia coli 3 0.7625
Beta-galactosidase P00722 BGAL_ECOLI Escherichia coli 3 0.7625
Purine nucleoside phosphorylase DeoD-type P0ABP8 DEOD_ECOLI Escherichia coli 3 0.7592
Purine nucleoside phosphorylase DeoD-type P0ABP8 DEOD_ECOLI Escherichia coli 3 0.7592
Actin, alpha skeletal muscle P68134 ACTS_MOUSE Mus musculus 4 0.7518
Actin, alpha skeletal muscle P68134 ACTS_MOUSE Mus musculus 4 0.7518
beta-glucosidase Q92AS9 Q92AS9_LISIN Listeria innocua serovar 6a 3 0.7283
beta-glucosidase Q92AS9 Q92AS9_LISIN Listeria innocua serovar 6a 3 0.7283
Regucalcin Q64374 RGN_MOUSE Mus musculus 3 0.7229
Regucalcin Q64374 RGN_MOUSE Mus musculus 3 0.7229
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 4 0.7199
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 4 0.7199
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 4 0.7190
Actin, alpha skeletal muscle P68135 ACTS_RABIT Oryctolagus cuniculus 4 0.7190
Glycogen phosphorylase, muscle form P00489 PYGM_RABIT Oryctolagus cuniculus 3 0.7122
Glycogen phosphorylase, muscle form P00489 PYGM_RABIT Oryctolagus cuniculus 3 0.7122
Iota toxin component Ia Q46220 Q46220_CLOPF Clostridium perfringens 4 0.7091
Iota toxin component Ia Q46220 Q46220_CLOPF Clostridium perfringens 4 0.7091
Beta-glucosidase 1A Q25BW5 BGL1A_PHACH Phanerodontia chrysosporium 3 0.7068
Beta-glucosidase 1A Q25BW5 BGL1A_PHACH Phanerodontia chrysosporium 3 0.7068
Glucosidase II subunit alpha Q9STC1 Q9STC1_GRALE Gracilariopsis lemaneiformis 3 0.7006
Glucosidase II subunit alpha Q9STC1 Q9STC1_GRALE Gracilariopsis lemaneiformis 3 0.7006

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